1 .TH g_nmens 1 "Thu 16 Oct 2008"
3 g_nmens - generates an ensemble of structures from the normal modes
8 .BI "-v" " eigenvec.trr "
9 .BI "-e" " eigenval.xvg "
10 .BI "-s" " topol.tpr "
11 .BI "-n" " index.ndx "
12 .BI "-o" " ensemble.xtc "
24 generates an ensemble around an average structure
25 in a subspace which is defined by a set of normal modes (eigenvectors).
26 The eigenvectors are assumed to be mass-weighted.
27 The position along each eigenvector is randomly taken from a Gaussian
28 distribution with variance kT/eigenvalue.
31 By default the starting eigenvector is set to 7, since the first six
32 normal modes are the translational and rotational degrees of freedom.
34 .BI "-v" " eigenvec.trr"
36 Full precision trajectory: trr trj cpt
38 .BI "-e" " eigenval.xvg"
44 Structure+mass(db): tpr tpb tpa gro g96 pdb
50 .BI "-o" " ensemble.xtc"
52 Trajectory: xtc trr trj gro g96 pdb
56 Print help info and quit
58 .BI "-nice" " int" " 19"
61 .BI "-[no]xvgr" "yes "
62 Add specific codes (legends etc.) in the output xvg files for the xmgrace program
64 .BI "-temp" " real" " 300 "
67 .BI "-seed" " int" " -1"
68 Random seed, -1 generates a seed from time and pid
70 .BI "-num" " int" " 100"
71 Number of structures to generate
73 .BI "-first" " int" " 7"
74 First eigenvector to use (-1 is select)
76 .BI "-last" " int" " -1"
77 Last eigenvector to use (-1 is till the last)